Import and Browse. Review data. bp_stages is a chart based on a graphic

Transcription

1 Import and Browse Review data is a chart based on a graphic hrs_clin is clinical data patient id (anonymized) some interesting things to note here. female is a boolean age is a number depress_dx is a 0/1, whether someone has been diagnosed bp_dx is a yes/no, whether someone has been diagnosed bp_rx is yes/no, whether someone has been prescribed bp medication systolic, diastolic readings and an id linking back to the (more on that later) hrs_genetic patient id polygen_map (genetic markers for mean arterial pressure) polyten_dep (genetic markers for depression) Data Cleanup Modify the data types discuss integer, numeric boolean, text Querying All : SELECT * One column SELECT bp_dia More than one SELECT id, bp_dia, bp_sys

2 DISTINCT SELECT bp_stage_id SELECT DISTINCT bp_stage_id ORDER BY SELECT DISTINCT bp_stage_id ORDER BY bp_stage_id NOTE: DESC for descending order, ASC for ascending (default if you don t specify it) Exercise : How many distinct ages are in the data set? How many distinct values for female? Example : what is our age range? SELECT DISTINCT age _sql ORDER BY age DESC This is a problem because of data issues! SELECT MAX(age), MIN(age) _sql ORDER BY age DESC we will get to this after filtering... Filtering SELECT * female = 'yes' Exercise : Select all rows where bp is at stage 2 inequalities SELECT * bp_sys > 120 More than one condition in a filter SELECT * bp_sys > 120 AND bp_dia > 80

3 you can use an OR clause as well SELECT * bp_sys > 120 OR bp_dia > 80 Exercise : Find all rows with low blood pressure SELECT * bp_sys <100 AND bp_dia < 60 Combining boolean clauses Mixing AND and OR SELECT * female = 'no' OR bp_stage_id = 4 AND bp_sys > 200 Now add parentheses around SELECT * (female = 'no' OR bp_stage_id = 4) AND bp_sys > 200 Note that the parentheses *can* matter Try counting the results, look at them. what s going on? The first one is applying the OR clause to the entire remainder of the query. With parentheses, it is only applied to a joint condition Solution, and advice - use parentheses. Sometimes they won t matter, sometimes they will (remember PEMDAS). It makes it readable, and you won t have to work through your own tricky logic. Remember, data can change, so no difference with one data set can become a difference one more data arrives! Yes, also, you may note that there is a redundant condition in the query above! Exercise: Find everyone with really low diastolic and systolic, or really high diastolic and systolic

4 SELECT * (bp_dia < 50 AND bp_sys < 100) OR (bp_dia > 110 AND bp_sys > 180) Add l: do the parenthese make any difference? in the results? to you? What if I wrote this? SELECT * bp_dia < 50 AND bp_sys < 100 OR bp_dia > 110 AND bp_sys > 180 It s about readability, not just what the computer does. IN SELECT * bp_stage_id IN (0, 2, 5) AGGREGATIONS SELECT female, COUNT(id) GROUP BY female SELECT female, AVG(age) GROUP BY female Can you get the AVG systolic by female? SELECT female, AVG(bp_sys) GROUP BY female (uncategorized is low! huh. I don t really know what to make of that) Exercise: Is it true for diastolic?

5 (maybe?) You can get more than one aggregation at a time SELECT age, COUNT(id), AVG(bp_dia) GROUP BY age HAVING SELECT age, COUNT(id), AVG(bp_dia) GROUP BY age HAVING count(id) > 50 You can group by more than one thing too SELECT female, age, count(id) GROUP BY female, age ORDERING SELECT female, age, count(id) GROUP BY female, age ORDER BY count(id) DESC Exercise Count the number of people who have or have not been diagnosed with bp SELECT bp_rx, count(bp_rx) GROUP BY bp_rx Count the number of people who have been diagnosed with bp by female(y/n) SELECT female, bp_rx, count(bp_rx) GROUP BY female, bp_rx

6 Feeling irritated with the null values? There are things you can do. SELECT female, bp_rx, count(bp_rx) female!= '' AND bp_rx!= '' GROUP BY female, bp_rx But the blank should probably be a NULL Data Cleaning UPDATE hrs_clin SET bp_rx = NULL where bp_rx = '' JOINS To join on stages through a common element SELECT *, You can now select and filter (and group) as if it were one table SELECT age, bp_sys, bp_dia, where high_blood_pressure = 'yes' AGGREGATIONS SELECT high_blood_pressure, count(hrs_clin.id), GROUP BY high_blood_pressure (note what happens if you don t use the alias) Exercise : get the average systolic and diastolic for people who have high blood pressure.

7 Exercise : How many people who have high blood pressure have been diagnosed? SELECT high_blood_pressure, bp_dx, count(hrs_clin.id), bp_dx!= '' GROUP BY high_blood_pressure, bp_dx check with smaller independent queries like this select count(1) where bp_dx = 'yes' and bp_stage_id > 2 ; joining multiple tables SELECT * FROM hrs_clin JOIN JOIN hrs_genetic ON hrs_clin.id = hrs_genetic.id